|
| Status |
Public on Jun 26, 2014 |
| Title |
Input_MEF_w8 |
| Sample type |
SRA |
| |
|
| Source name |
Mouse Embryonic Fibroblasts
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Mouse Embryonic Fibroblasts
chip antibody: none (Input)
genotype: wt
|
| Growth protocol |
ES cells were grown on gelatin coated plates with ES medium ( DMEM supplemented with 15% FCS, 1x Pen/strept, L-Glutamine 2mM, ß-mercaptoethanol 0.1 MM, Non Essential amino acids 1x, Sodium piruvate 1mM and LIF). MEFs were grown in DMEM supplemented with 10% FCS, 1x Pen/strept, L-Glutamine 2mM, ß-mercaptoethanol 0.1 MM, Non Essential amino acids 1x, Sodium piruvate 1mM. In vitro differentiation to NPCs was carried out as described before (Bibel et al., 2007)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
For ChIP, double cross-linking with Di(N-succinimidyl)-glutarate and formaldehyde was used as described (Nowak et al., 2005). After sonication, lysates were incubated with the corresponding antibodies, histones-DNA complexes were immunoprecipitated with dynabeads and DNA was purified using columns.
Libraries were prepared following the standard illumina Pair-end protocol.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
two biological replicates
Raw files for Rep 1: W8_input_NoIndex_L003_R1_001.fastq.gz ; W8_input_NoIndex_L003_R2_001.fastq.gz
Raw files for Rep 2: W8_input_NoIndex_L007_R1_001.fastq.gz ; W8_input_NoIndex_L007_R2_001.fastq.gz
|
| Data processing |
Illumina Casava 1.7.0 and bcl2fastq 1.8.3 software used for basecalling.
Bowtie version 2.0.0-beta6 with parameters -D 15 -R 2 -N 0 -L 32 -i S,1,0.75 -M 10000 was used to map reads agains the mm9 genome build. The default bowtie2 mapping of multi-reads to one of the possible genomic locations was used. Reads mapping with mismatches were removed.
For each ChIP-seq the number of reads overlapping a region of 10bp was normalized by the total number of reads sequenced. The difference between the ChIP normalized counts and the Input is reported. The tool bamCompare from the deepTools package (http://deeptools.github.io) was used to compute the differences.
bigWig difference ChIP vs. Input files (-input_merge.bw) were generated using bamCompare from the deepTools package (http://deeptools.github.io). Scores represent the ChIP-seq normalized number of reads minus the input normalized number of reads overlaping bins of 10bp.
bigWig normalized signal files (-merge.bw) were generated using bamCoverage from the deepTools package (http://deeptools.github.io). Scores represent the normalized number of reads overlaping bins of 10bp. The normalization scales the original depth of sequencing to match a depth of 1x.
Genome_build: mm9
|
| |
|
| Submission date |
Apr 25, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Thomas Manke |
| Organization name |
Max-Planck-Institute for Immunobiology and Epigenetics
|
| Department |
Bioinformatics and Deep-Sequencing Unit
|
| Street address |
Stuebeweg 51
|
| City |
Freiburg im Breisgau |
| ZIP/Postal code |
79108 |
| Country |
Germany |
| |
|
| Platform ID |
GPL9250 |
| Series (1) |
| GSE57092 |
Suv39h-dependent H3K9me3 represses intact retrotransposons in mouse embryonic stem cells |
|
| Relations |
| BioSample |
SAMN02737346 |
| SRA |
SRX527858 |
